BackThe Chemical Context of Life: Essential Chemistry for Biology
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Chapter 2: The Chemical Context of Life
Chemistry of Life: Creating Compounds
All living organisms are composed of matter, which is anything that occupies space and has mass. The study of chemistry is fundamental to understanding biological processes because life depends on chemical interactions and compounds.
Element: A substance that cannot be broken down into other substances by chemical means.
Atom: The smallest unit of an element that retains its chemical properties.
Compound: A substance consisting of two or more elements in a fixed ratio, exhibiting emergent properties distinct from its constituent elements.
Example: Sodium (Na) and chlorine (Cl) combine to form sodium chloride (NaCl), a compound with properties different from its elements.
Elements of Life
Of the 92 naturally occurring elements, only about 20-25% are essential for life. These essential elements are required for an organism to survive, grow, and reproduce. Trace elements are needed in minute quantities but are still vital for biological functions.
Example: Iodine is required for thyroid function; its deficiency can cause goiter in humans.
Evolution of Tolerance to Toxic Elements
Some elements are toxic to most organisms, but certain species have evolved mechanisms to tolerate or even utilize these elements. This adaptation can be harnessed for environmental cleanup.
Phytoremediation: The use of plants, such as sunflowers, to absorb and detoxify heavy metals from contaminated soils.
Example: Sunflowers were used to clean up soils contaminated with heavy metals after environmental disasters.
Element Properties Depend on Atomic Structure
Atomic Structure
Atoms are composed of three types of subatomic particles: neutrons (no charge), protons (positive charge), and electrons (negative charge). The protons and neutrons form the atomic nucleus, while electrons occupy regions called electron shells around the nucleus.
Atomic Number and Atomic Mass
The identity and properties of an element are determined by the number of protons in its nucleus (atomic number). The mass number is the sum of protons and neutrons. Atomic mass is approximately equal to the mass number.
Atomic number (Z): Number of protons in the nucleus.
Mass number (A): Number of protons plus neutrons.
Number of neutrons: Mass number minus atomic number.
Formulas:
Isotopes
Isotopes are different forms of the same element, having the same number of protons but different numbers of neutrons. Some isotopes are radioactive, meaning their nuclei decay spontaneously, emitting particles and energy.
Applications: Radioactive isotopes are used in dating fossils, tracing metabolic pathways, and diagnosing medical disorders (e.g., PET scans).
Hazards: Radiation from decaying isotopes can damage cellular molecules.
Energy and Electrons
Energy Levels of Electrons
Energy is the capacity to cause change. Electrons possess potential energy due to their position relative to the nucleus. Electrons can move between energy levels (shells) by absorbing or releasing energy.
Electrons in higher shells have more potential energy.
Energy is absorbed to move to a higher shell and released when moving to a lower shell.
Electron Shells and Chemical Bonds
The chemical behavior of an atom is determined by the number of electrons in its outermost shell (valence shell). Atoms with incomplete valence shells are reactive and can form chemical bonds by sharing or transferring electrons.
Chemical Bonds and Interactions
Covalent Bonds
A covalent bond involves the sharing of a pair of valence electrons between two atoms. Molecules are formed when two or more atoms are held together by covalent bonds. Covalent bonds can be single (one pair shared) or double (two pairs shared).
Electronegativity and Polar Covalent Bonds
Electronegativity is the tendency of an atom to attract electrons in a covalent bond. When atoms differ in electronegativity, the shared electrons are distributed unequally, resulting in a polar covalent bond.
Polar covalent bond: Electrons are shared unequally, creating partial charges (e.g., in water molecules).
Ionic Bonds
Ionic bonds form when one atom transfers electrons to another, resulting in oppositely charged ions (cations and anions) that attract each other. Ionic compounds are often called salts.
Cation: Positively charged ion (lost electron).
Anion: Negatively charged ion (gained electron).
Weak Chemical Interactions
Many biological molecules are stabilized by weak interactions, including hydrogen bonds and van der Waals interactions.
Hydrogen bond: A weak attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.
Van der Waals interactions: Weak attractions due to transient local partial charges, significant when many such interactions occur together.
Chemical Reactions
Making and Breaking Chemical Bonds
Chemical reactions involve the making and breaking of chemical bonds, transforming reactants into products. Photosynthesis is a key example of a biological chemical reaction:
Water and Life
Hydrogen Bonding and Water
Water is a polar molecule, and hydrogen bonding between water molecules is responsible for many of its unique properties essential for life, such as cohesion, adhesion, surface tension, and its role as a solvent.
Cohesion and Adhesion
Cohesion refers to the attraction between water molecules due to hydrogen bonding, while adhesion is the attraction between water molecules and other substances. These properties are crucial for water transport in plants.
Surface Tension
Surface tension is a measure of how difficult it is to stretch or break the surface of a liquid. Water has a high surface tension due to hydrogen bonding, allowing small organisms to move across its surface.
Moderation of Temperature by Water
Water can absorb or release large amounts of heat with only slight changes in its own temperature, helping to stabilize environmental and biological temperatures.
Floating of Ice on Liquid Water
Ice is less dense than liquid water because hydrogen bonds in ice are more ordered, causing it to float. This property insulates aquatic environments, allowing life to persist under ice-covered surfaces.
Water: The Solvent of Life
Water is an excellent solvent due to its polarity, allowing it to dissolve many ionic and polar substances. Solutions in which water is the solvent are called aqueous solutions.
Solvent: The dissolving agent.
Solute: The substance dissolved.
Hydrophilic: Substances with an affinity for water.
Hydrophobic: Substances that do not interact with water (often nonpolar).
Acids, Bases, and pH
Acids, Bases, and Buffers
Acids increase the concentration of hydrogen ions (H+) in a solution, while bases decrease it. The pH scale measures the concentration of H+ ions, with most biological fluids having a pH between 6 and 8. Buffers help maintain stable pH by accepting or donating H+ ions as needed.
Acid: pH < 7
Base: pH > 7
Buffer: Minimizes changes in H+ or OH- concentration.
